Areas hosting hotspots of low‐latitude marginal populations of cold‐adapted plant species could be key areas for understanding geographical attributes that result in refugia during climatic shifts as well as the conservation of genetic diversity in the face of climate change. Low‐latitude populations of cold‐adapted plants are important because they may harbour the combination of alleles that foster persistence in a warmer climate. Consequently, identification of areas where arctic‐alpine, circumpolar and circumboreal species reach the low‐latitude ends of their distribution will present a unique opportunity to uncover processes that shaped current biogeographical patterns, as well as prepare for future scenarios. Here, we identify 35 main marginal population hotspots (19 and 16 areas in North America and Europe, respectively) of 183 plant taxa. These hotspots represent areas where southern marginal populations of cold‐adapted species co‐occur. The identification of hotspots was based on geographic overlap of southernmost locations of the target species, in a 50 × 50 km grid. With a threshold of two species in a single grid cell or in two contiguous cells, the analysis revealed that hotspots are in most cases located in the southern portion of major mountain chains. However, hotspots also occur in lowland areas at high latitudes (Fennoscandia, Alaska, Hudson Bay) which do not necessarily correspond to known cold‐ or warm‐stage refugia (e.g. Alps). Rockies and Sierra Nevada both in California and Spain, Apennines, and the southern Scandes, maintain their hotspot status even with more stringent cut‐off thresholds (>3 and >5 species per cell group). From a conservation point of view, our analysis reveals that only a small portion of the hotspots are currently included within protected areas. We discuss the importance of marginal population hotspots to future research on climate change and, finally, outline how conservation strategies can capitalize on the knowledge gained from studying climate change effects on cold‐adapted plants.